One thing you can do is hide all of the Mono-To-Stereo versions of the plug-ins as these don't work properly in SONAR anyway. I seem to recall that they basically just lock the track down to mono and then only output one channel. You can verify this using any of the plugins like H-Delay or SuperTap and noting that the audio is all kinds of messed up when you pan out the delay taps. To do mono-to-stereo in SONAR, you use enable stereo interleave on the track and then insert the Stereo versions of the Waves plug-ins.
Most of the Mono versions can also be hidden as the processing will be identical using the Stereo version on mono tracks assuming the two channels are processed independently. I'd guess that is the case for anything in Gold other than maybe the V-series. A while ago, I actually did comparisons for my favorite plug-ins where I generated wave files using both versions for mono audio and the output was bit exact other than for some of the vintage style plug-ins that insert noise and maybe do some other cross-channel processing (and may also be functionally equivalent but just different due to the randomness of the noise). I believe the Mono versions are holdovers from back in the 90s when Waves was trying to squeeze out every tiny bit of CPU and RAM available. On modern systems, the difference is not something you will ever notice and not worth the hassle of having the extra plug-ins around and the hassle of converting over to stereo at a later date (i.e. delete the Mono plug-in, add the Stereo, and then recreate your settings).